At the turn of the millennium, Ginei Studio's dilapidated buildings are set to be demolished. Ex-employee and filmmaker Genya Tachibana decides to honor this occasion with a commemorative documentary about the company's star actress: Chiyoko Fujiwara, the reclusive sweetheart of Shouwa Era cinema. Having finally obtained permission to interview the retired starlet, an enamored Genya drags along cynical cameraman Kyouji Ida to meet her, ready to put his lifelong idol back in the spotlight once more. Hidden in this secluded mountain retreat is a thousand years of history condensed into one lifetime, waiting to be narrated. Chiyoko's recollections take them on an illusionary journey through Japanese cinematic history that transcends the boundaries of reality; the saga of her acting career intertwines with her filmography, the actors in her life blend seamlessly with the characters on screen, and the present melds with the past. Though the actress may have retired at the height of her career 30 years ago, the curtain on her life's stage has yet to fall.

Yukiteru Amano is a shy middle schooler who regularly keeps track of what he does in his daily life by writing down all of his activities on his phone—a digital diary. Despite having no friends at school, Yukiteru is frequently seen talking to his supposedly imaginary friends Deus Ex Machina, the god of time and space; and Deus' servant, Mur Mur. One day, Yukiteru wakes up and discovers that certain events of his day are preemptively displayed on his cellphone. While initially dismissing it as a coincidence, he slowly realizes that the incidents written in his phone actually take place in the near future. After spending the day benefiting from this new asset, Yukiteru learns that his classmate Yuno Gasai possesses a similar diary. As the two team up to defeat an odd pursuer and head back to their respective homes, Deus Ex Machina explains that they—alongside 10 other contestants—have been drawn into a survival game whose victor will become the deity's successor. With no other options, Yukiteru and Yuno must use their cellphones—now called Future Diaries—to survive this unforgiving battle royale.

By the year 0096 of the Universal Century, a fragile peace emerges from the ashes of conflict. Sixteen-year-old student Banagher Links visits the Industrial 7 space colony on a school field trip, but because of a broken shuttle, he is left completely stranded. To Banagher, who has always lived a normal life, war had always been a distant, almost mythical part of history; but within minutes, fantasy becomes reality when he rescues a girl named Audrey Burne, who urgently needs to meet with the leader of the nearby Vist Foundation, Cardeas Vist. She hopes to persuade him to withhold the Laplace's Box, an object that holds the potential to destroy the world. History is set in motion as galactic forces converge on Industrial 7, each vying for possession of the Laplace's Box. As Neo Zeon remnants clash with Earth Federation Forces around the colony, Cardeas, in his final moments, gives Banagher the key to the Box, a mobile suit dubbed The Unicorn Gundam. Packed with explosive action and rising tension, Mobile Suit Gundam Unicorn RE:0096 follows Banagher as his conviction is tested and the destiny that has laid dormant for more than a century is finally realized.

In the year Universal Century 0096, three years after Char Aznable's failed attempt to force human migration into space, life continues in the colonies orbiting Earth. One such colony, at Side 4, is home to Banagher Links, a 16-year-old who lives a quiet life among his classmates. Audrey Burne, the last descendant of a great tyrannical family, takes it upon herself to steal the key to a mysterious device known as Laplace's Box. It is said that the Box has the power to shape the course of the universe, and Audrey travels to Side 4 in an attempt to take it from its current holder and keep it from the Sleeves, the surviving remnant of Char Aznable's Neo-Zeon. In her search, she stumbles across Banagher and changes his life forever. When Side 4 comes under the attack of the Sleeves and its prolific fighters Marida Cruz and Full Frontal, Banagher takes control of the newly built Gundam Unicorn to defend his friends and protect the fate of humankind.